COMPLEX PATTERNS

Do you know anything about the manner in which the artifacts are
produced? For example, one might imagine that the observed frequency of
allele 1 is a linear mixture of the real frequency and the frequency of
other alleles, say obs(a1) = c1*a1+c2*a2+c3*a3+ +. You would have a
system of such equations which can be solved given enough constraints on
the coefficients ci. You can do things similar to this with more
complicated mixture models. But more information is needed before we can
suggest something...